|
| Status |
Public on Jan 23, 2012 |
| Title |
Col-0, Salt-treated plants, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Salt-treated Arabidopsis Col-0 plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: wildtype
ecotype: Columbia
tissue: Whole plants
treatment: salt
age: 11 day old seedlings
|
| Treatment protocol |
The 10-d-old plants were transfered onto 1/2 MS agar plates without sucrose containing either 0 or 200 mM NaCl and then incubated for 24 hours.
|
| Growth protocol |
Arabidopsis thaliana WT and ipt1,3,5,7 mutant plants (Columbia ecotype) were grown on GM agar (0.8%) medium supplemented with 3% sucrose for 10 days (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the salt-treated or untreated plants using TRIzol Reagent (Invitrogen) according to the manufacturer’s instruction.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression data from salt-treated Col-0 plants
|
| Data processing |
The scanned images were analyzed with GeneSpring ver.11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.
|
| |
|
| Submission date |
Sep 13, 2011 |
| Last update date |
Jan 23, 2012 |
| Contact name |
Rie Nishiyama |
| Organization name |
RIKEN
|
| Department |
Plant Science Center
|
| Lab |
Signaling Pathway Research Unit
|
| Street address |
Suehiro-cho 1-7-22, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE32087 |
Expression data in an Arabidopsis cytokinin-deficient mutant, ipt1,3,5,7 and its wild type plant (Col-0) under high salinity and control conditions. |
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